Methods for analyzing polynucleotide sequences can be grouped to two major fields: electrophoretic and non-electrophoretic methods. The electrophoretic methods include slab gel electrophoresis, capillary electrophoresis, microfabricated capillary arrays, and free solution electrophoresis. All these methods rely on the Sanger method in which polynucleotide chain elongation inhibitors are incorporated into the polynucleotide strands which are then separated according to their sizes, usually on a polyacrylamide gel. These methods are the common means for analyzing polynucleotide sequences nowadays. However, the process is time-consuming, requires large amount of target polynucleotides and reaction reagents, and has limited ability to read long sequences that are inherent in the gel electrophoresis methods. The non-electrophoretic methods include pyrosequencing, sequencing by hybridization, massively parallel signature sequencing, and sequencing by mass spectrometry. These methods also have a number of disadvantages. For example, they usually require synchronization of the polynucleotide templates which inevitably decay with each cycle of sequencing reaction.
Thus, there is a need in the art for better methods for analyzing polynucleotide sequences, e.g., methods with high throughput, parallelism, and resolution. The present invention fulfills this and other needs.